Before I add my request just let me said that I been using wordpress for a while and I think is great!!! keep up the great work.
Now my request. It looks like that when I save my images in a custom location not in the "uploads" folder I not able to edit (crop, rotate flip) the image, I can see the images just fine but I am not able to edit it using wordpress.
I seems to be something to do with the "_wp_attached_file" postmeta entry in the database, because the image edit uses "wp-content/uploads" as root instead of "wp-content" basically if you delete "_wp_attached_file" in the database or if the image is outside the "uploads" folder it doesn't work it will be neat to be able to use custom image location and to be able to edit it.
Other thing if you decide to change your image folder location the "_wp_attached_file" entry breaks the image preview completely if I delete the database entry it works just fine but still can't edit.